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05-14-2013, 07:53 AM
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Member
Location: GERMANY Join Date: Apr 2013
Posts: 16
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samtools mpileup
Hey guys,
i`m new to the field of ngs and have a question regarding the mpileup option -M: -M INT cap mapping quality at INT [60] i dont get the need of this option. Why is it necessary to cap a mapping quality of 60? Its in my opinion a good value... And what is ment by cap? Does this means, that this read is totally ignored becaus its mapping quality is exactly 60?! I have realy no clue of the consequence of this option. So without mentioning this option each read having a mapping quality of 60 is ignored? :/ i hope someone can help me out here... oh still one question:) is there anywhere a detailed description of the ALL parameters? the manual http://samtools.sourceforge.net/samtools.shtml seems to exmplain only a part of all parameters in detail... Many thanks in advance:) volavii |
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| mapping quality scores, mpileup, samtools |
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